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OliveiraDS-hub / ChimeraTE

A pipeline to detect chimeric transcripts derived from genes and transposable elements.
GNU General Public License v3.0
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How to understand the meaning of exonized_type? #7

Closed Orz-CQ closed 10 months ago

Orz-CQ commented 10 months ago

Hi,

I am confused about how to understand the exonized_type. What are the meaning of "Embedded", "Overlapped" and "Intronic".

If the "Intronic" means the TEs insert into the intron, and support by the chimeric reads? If the "Embedded" means the TEs insert into the whole gene region and may cross both the exon and intron region?

Thanks in advance!

Lan

OliveiraDS-hub commented 10 months ago

Hi @Orz-CQ!

The exonized type is regarding the position of the TE insertion compared to the exons. All exonizations are supported by chimeric reads.

The classification is demonstrated on the supp. figure 1 of our paper:

mm_figure_FINAL

Let me know if it's clear now, then I can close the issue

Orz-CQ commented 10 months ago

Sorry I cannot find this supp. figure1 from the bioRxiv. This plot has completely answer my questions. Thanks for your quickly response!

OliveiraDS-hub commented 10 months ago

Probably you are looking for ir in the first version of the manuscript. On BioRxiv, check if there is a red button "View current version of this article" on the top-left of the title, or check it out here:

https://www.biorxiv.org/content/10.1101/2022.09.05.505575v2

The figure is in the docx file in the supp material.

Thank you for your feedback! I'm closing this issue. Do not hesitate to open another if have questions.

Best